Laboratory experiments provide no general answer to the question of whether zooplankton affects cyanobacteria or are affected by prokaryotes. A cyanobacterium may be grazed upon as small colonies, and the same species, as larger colonies, may inhibit zooplankton feeding. Within zooplankton, different species or groups may be affected differently. With this background we set out to detect winter zooplankton grazing and toxicity of overwintering populations of Microcystis aeruginosa. A polymerase chain reaction (PCR) method with oligonucleotide primers for the mcy gene cluster that encodes microcystin synthetase was employed for detection of M. aeruginosa reminiscent products in grazing cladocera. In our field studies, we detected the mcy gene cluster in strains of overwintering colonies of benthic Microcystis and also confirmed the expression of toxicity by quantitative PCR, phosphatase inhibition and enzyme-linked immunosorbent assays (ELISA). We further confirmed the presence of the mcy gene cluster in DNA and RNA isolated from sampled Daphnia magna specimens, indicating that zooplankton in the natural environment may ingest toxic Microcystis cells as part of their diet during winter months.